Bulk tissue RNA-seq of in vitro macaque fetal cortical neural stem cells

Early telencephalic development involves patterning of the distinct regions and fate specification of the neural stem cells (NSCs). These processes, mainly characterized in rodents, remain elusive in primates and thus our understanding of conserved and species-specific features. Here, we profiled 761,529 single-cell transcriptomes from multiple regions of the prenatal macaque telencephalon. We defined the molecular programs of the early organizing centers and their cross-talk with NSCs, finding primatebiased signaling active in the antero-ventral telencephalon. Regional transcriptomic divergences were evident at early states of neocortical NSC progression and in differentiated neurons and astrocytes, more than in intermediate transitions. Finally, we show that neuropsychiatric disease- and brain cancerrisk genes have putative early roles in the telencephalic organizers’ activity and across cortical NSC progression. Macaque cortical region specific NSCs were expanded in vitro for 5 days (DIV 5). Differentiation was induced after DIV5 and cells were grown until DIV20. Total RNA was extracted at NSC state (DIV1-5), differentiation transition DIV (6-8) and terninal differentiation (DIV11-20).